filtering {GenomicDataCommons} | R Documentation |
Manipulating GDCQuery filters
The filter
is simply a safe accessor for
the filter element in GDCQuery
objects.
The get_filter
is simply a safe accessor for
the filter element in GDCQuery
objects.
filter(x, expr) ## S3 method for class 'GDCQuery' filter(x, expr) get_filter(x) ## S3 method for class 'GDCQuery' get_filter(x)
x |
the object on which to set the filter list member |
expr |
a filter expression in the form of
the right hand side of a formula, where bare names
(without quotes) are allowed if they are available
fields associated with the GDCQuery object, |
A GDCQuery
object with the filter
field replaced by specified filter expression
# make a GDCQuery object to start # # Projects # pQuery = projects() # check for the default fields # so that we can use one of them to build a filter default_fields(pQuery) pQuery = filter(pQuery,~ project_id == 'TCGA-LUAC') get_filter(pQuery) # # Files # fQuery = files() default_fields(fQuery) fQuery = filter(fQuery,~ data_format == 'VCF') # OR # with recent GenomicDataCommons versions: # no "~" needed fQuery = filter(fQuery, data_format == 'VCF') get_filter(fQuery) fQuery = filter(fQuery,~ data_format == 'VCF' & experimental_strategy == 'WXS' & type == 'simple_somatic_mutation') files() %>% filter(~ data_format == 'VCF' & experimental_strategy=='WXS' & type == 'simple_somatic_mutation') %>% count() files() %>% filter( data_format == 'VCF' & experimental_strategy=='WXS' & type == 'simple_somatic_mutation') %>% count() # Filters may be chained for the # equivalent query # # When chained, filters are combined with logical AND files() %>% filter(~ data_format == 'VCF') %>% filter(~ experimental_strategy == 'WXS') %>% filter(~ type == 'simple_somatic_mutation') %>% count() # OR files() %>% filter( data_format == 'VCF') %>% filter( experimental_strategy == 'WXS') %>% filter( type == 'simple_somatic_mutation') %>% count() # Use str() to get a cleaner picture str(get_filter(fQuery))